def _plotHistogram(self, param=None):
md = MetaData()
md.read(self.protocol._getFileName(FN_METADATA_HISTOGRAM))
x_axis = []
y_axis = []
i = 0
for idx in md:
x_axis_ = md.getValue(MDL_X, idx)
if i == 0:
x0 = x_axis_
elif i == 1:
x1 = x_axis_
y_axis_ = md.getValue(MDL_COUNT, idx)
i += 1
x_axis.append(x_axis_)
y_axis.append(y_axis_)
delta = x1 - x0
fig = plt.figure()
plt.bar(x_axis, y_axis, width=delta)
plt.title("Resolutions Histogram")
plt.xlabel("Resolution (A)")
plt.ylabel("Counts")
return [Plotter(figure2=fig)]
def _plotHistogram(self, fnhist, titlename, xname):
md = MetaData()
md.read(self.protocol._getPath('extra/' + fnhist))
x_axis = []
y_axis = []
i = 0
for idx in md:
x_axis_ = md.getValue(MDL_X, idx)
if i == 0:
x0 = x_axis_
elif i == 1:
x1 = x_axis_
y_axis_ = md.getValue(MDL_COUNT, idx)
i += 1
x_axis.append(x_axis_)
y_axis.append(y_axis_)
delta = x1 - x0
plt.figure()
plt.bar(x_axis, y_axis, width=delta)
plt.title(titlename + "Histogram")
plt.xlabel(xname + "(a.u.)")
plt.ylabel("Counts")
return plt.show()
def _plotHistogram(self, param=None):
md = MetaData()
md.read(self.protocol._getPath('extra/hist.xmd'))
x_axis = []
y_axis = []
i = 0
for idx in md:
x_axis_ = md.getValue(MDL_X, idx)
if i==0:
x0 = x_axis_
elif i==1:
x1 = x_axis_
y_axis_ = md.getValue(MDL_COUNT, idx)
i+=1
x_axis.append(x_axis_)
y_axis.append(y_axis_)
delta = x1-x0
plt.figure()
plt.bar(x_axis, y_axis, width = delta)
plt.title("Resolutions Histogram")
plt.xlabel("Resolution (A)")
plt.ylabel("Counts")
return plt.show()
def _plotHistogram(self, param=None):
md = MetaData()
md.read(self.protocol._getPath('extra/hist.xmd'))
x_axis = []
y_axis = []
i = 0
for idx in md:
x_axis_ = md.getValue(MDL_X, idx)
if i == 0:
x0 = x_axis_
elif i == 1:
x1 = x_axis_
y_axis_ = md.getValue(MDL_COUNT, idx)
i += 1
x_axis.append(x_axis_)
y_axis.append(y_axis_)
delta = x1 - x0
plt.figure()
plt.bar(x_axis, y_axis, width=delta)
plt.title("Resolutions Histogram")
plt.xlabel("Resolution (A)")
plt.ylabel("Counts")
return plt.show()
def _plotHistogram(self, param=None):
md = MetaData()
md.read(self.protocol._getFileName(FN_METADATA_HISTOGRAM))
x_axis = []
y_axis = []
for idx in md:
x_axis_ = md.getValue(MDL_X, idx)
y_axis_ = md.getValue(MDL_COUNT, idx)
x_axis.append(x_axis_)
y_axis.append(y_axis_)
plotter = EmPlotter()
plotter.createSubPlot("Resolutions Histogram", "Resolution (A)",
"# of Counts")
barwidth = (x_axis[-1] - x_axis[0]) / len(x_axis)
plotter.plotDataBar(x_axis, y_axis, barwidth)
return [plotter]
def _showColorSlices(self, fileName, setrangelimits, titleFigure, lowlim,
highlim):
imageFile = self.protocol._getExtraPath(fileName)
img = ImageHandler().read(imageFile)
imgData = img.getData()
imgData2 = np.ma.masked_where(imgData < 0.001, imgData, copy=True)
if setrangelimits is True:
fig, im = self._plotVolumeSlices(titleFigure,
imgData2,
lowlim,
highlim,
self.getColorMap(),
dataAxis=self._getAxis())
else:
md = MetaData()
md.read(self.protocol._getExtraPath(OUTPUT_THRESHOLDS_FILE))
idx = 1
val1 = md.getValue(MDL_RESOLUTION_FREQ, idx)
val2 = md.getValue(MDL_RESOLUTION_FREQ2, idx)
if val1 >= val2:
max_Res = val1 + 0.01
else:
max_Res = val2
# max_Res = np.nanmax(imgData2)
min_Res = np.nanmin(imgData2)
fig, im = self._plotVolumeSlices(titleFigure,
imgData2,
min_Res,
max_Res,
self.getColorMap(),
dataAxis=self._getAxis())
cax = fig.add_axes([0.9, 0.1, 0.03, 0.8])
cbar = fig.colorbar(im, cax=cax)
cbar.ax.invert_yaxis()
return plt.show(fig)
